Sting_RDB: a relational database of structural parameters for protein analysis with support for data warehousing and data mining

An effective strategy for managing protein databases is to provide mechanisms to transform raw data into consistent, accurate and reliable information. Such mechanisms will greatly reduce operational inefficiencies and improve one's ability to better handle scientific objectives and interpret the research results. To achieve this challenging goal for the STING project, we introduce Sting_RDB, a relational database of structural parameters for protein analysis with support for data warehousing and data mining. In this article, we highlight the main features of Sting_RDB and show how a user can explore it for efficient and biologically relevant queries. Considering its importance for molecular biologists, effort has been made to advance Sting_RDB toward data quality assessment. To the best of our knowledge, Sting_RDB is one of the most comprehensive data repositories for protein analysis, now also capable of providing its users with a data quality indicator. This paper differs from our previous study in many aspects. First, we introduce Sting_RDB, a relational database with mechanisms for efficient and relevant queries using SQL. Sting_rdb evolved from the earlier, text (flat file)-based database, in which data consistency and integrity was not guaranteed. Second, we provide support for data warehousing and mining. Third, the data quality indicator was introduced. Finally and probably most importantly, complex queries that could not be posed on a text-based database, are now easily implemented. Further details are accessible at the Sting_RDB demo web page: http://www.cbi.cnptia.embrapa.br/StingRDB.     

Leaf functional traits and monodominance in Southern Amazonia tropical forests

Tropical monodominant forests are rare communities with low tree species diversity. Species monodominance is not the product of a single mechanism, but the result of a set of not yet fully understood integrated ecological factors acting together. We compared populations of Brosimum rubescens in monodominant and mixed forests in Southern Amazonia to test whether leaf functional traits are ecological factors related to monodominance. Individuals of B. rubescens in the mixed forest invest in conservative strategies, while those in the monodominant forest invest in acquisitive strategies. Leaf functional traits, such as petiole length and adaxial cuticle thickness, could be associated with the monodominance of B. rubescens. Our study highlights for the first time the power of integrating leaf functional traits as a component of the set of ecological conditions to explain species monodominance. B. rubescens showed different functional strategies to establish and maintain its population in different forests, which makes it a strong competitor for resources, such as water and light, through variation in its leaf functional traits. We also suggest that such high plasticity can be an important condition for the persistence of the species over time.

     

Epiphytic cyanobacterial strains in the roots of Salvinia auriculata and the effect of light and nutrients on the production of heterocyst,akinete and hormogonia

Aquatic Ecology - In epiphytic associations, cyanobacteria form the periphyton with phytoplanktonic algae and with aquatic macrophytes. In this study, we found homocytous and heterocytous...     

Electrophysiological characterization of Tityus obscurus β toxin 1 (To1) on Na+-channel isoforms

To1, previously named Tc49b, is a peptide neurotoxin isolated from venom of the scorpion Tityus obscurus that is responsible for lethal human poisoning cases in the Brazilian Amazonian region. Previously, To1 was shown to be lethal to mice and to change Na⁺ permeation in cerebellum granular neurons from rat brain. In addition, To1 did not affect Shaker B K⁺ channels. Based on sequence similarities, To1 was described as a β-toxin. In the present work, To1 was purified from T. obscurus venom and submitted to an electrophysiological characterization in human and invertebrate Na_V channels. The analysis of the electrophysiological experiments reveal that To1 enhances the open probability at more negative potentials of human Na_V 1.3 and 1.6, of the insect channel BgNa_V1 and of arachnid VdNa_V1 channel. In addition, To1 reduces the peak of Na⁺ currents in some of the Na_Vs tested. These results support the classification of the To1 as a β-toxin. A structure and functional comparison to other β-toxins that share sequence similarity to To1 is also presented.     

Atlantic Forest topsoil nutrients can be resistant to disturbance and forest clearing

Human impacts can affect the soil properties through erosion and leaching, the ecosystem functions and, consequently, the capacity of a forest to regenerate. Here, we determine the effects of forest disturbance and succession on selected soil chemical properties using two different approaches, before‐after‐control‐impact (BACI) and space‐for‐time (SFT) substitution, and the threatened Atlantic Forest biome as model. We assessed with BACI the long‐term (37‐year) effects of clear cutting on soil properties by comparing data from two topsoil surveys (1978–2017) divided into two treatments: a preserved old growth forest (control) and an adjacent forest that was experimentally cleared with full tree removal (clear‐cut). We examined with SFT the relationship between stand age and soil properties using soil data from three old growth and 13 s growth forests ranging from 7 to 33 years. We found no significant differences between treatments for any soil property or significant changes in phosphorus, potassium, and calcium + magnesium over time. In contrast, pH increased and aluminum decreased in both areas. No relation was found between forest age and most of soil properties, with the exception of potassium which returned to old growth forest levels after 20 years of natural succession, and pH. BACI indicated that deforestation of old growth forest caused no significant effects on soil chemical properties after 37 years of regeneration. SFT demonstrated that soil properties did not change significantly during forest regeneration on formerly disturbed lands. Our findings indicate that natural nutrient‐depleted lowland forests were overall resistant to deforestation followed by passive regeneration at landscape scale. Abstract in Portuguese is available with online material.     

Coastal zone use and migratory behaviour of the southern population of Mugil liza in Brazil

We analysed the ratios Sr:Ca and Ba:Ca in the otoliths of 55 adults of the southern population of Mugil liza in Brazil (Paraná to Rio Grande do Sul) to investigate its coastal zone use and migratory behaviour. All individual M. liza analysed had Sr:Ca and Ba:Ca values indicating that their birth was in the marine environment, which is consistent with the southern population migration to spawn in the ocean,. Juveniles exhibited at least three coastal use and recruitment strategies (contingents): the majority (89%) of M. liza juveniles migrated toward brackish water. They entered the estuary before completing the first year of life (64%) or after (25%) their first year of life. The remaining 11% did not appear to enter brackish or freshwater water as a nursery or at any point in their life cycle. Some adults returned to the estuary after spawning in the ocean but others (of both sexes) never returned to the estuary after spawning, remaining in the marine environment. The pattern of juvenile habitat use in the Brazilian southern population of M. liza seems to be recurrent throughout the extent of its distribution as a consequence of the reproductive spawning aggregation behaviour, which mixes all contingents (with marine or estuarine preferences).     

Deep-water fisheries along the British Isles continental slopes: status,ecosystem effects and future perspectives

In this paper, we revisit the state of deep-water fisheries to the west of the British Isles and aim to provide an overview on the key drivers behind community changes along continental margins. The deep-water fisheries to the west of the British Isles that extend from the shelf-slope break down to the lower slope and along banks and seamounts of the Rockall Basin, mainly target blue ling Molva dypterygia, roundnose grenadier Coryphaenoides rupestris, orange roughy Hoplostethus atlanticus, with by-catches of black scabbardfish Aphanopus carbo and tusk Brosme brosme. These fishing grounds experienced a long period of exhaustive exploitation until the early 2000s, but subsequently the implementation of management strategies has helped to relieve excessive fishing pressure. It is widely accepted that a better understanding of the long-term implications of disturbance is needed to understand patterns in deep-water communities and what sustainable use and exploitation of resources might look like in this context.     

Identification of Biomarkers of Mercury Contamination in Brachyplatystoma filamentosum of the Madeira River,Brazil, Using Metalloproteomic Strategies

Biological Trace Element Research - Predator fish can accumulate high levels of mercury, which qualifies them as potential indicators of this toxic metal. The predatory species Brachyplatystoma...